Nikolaos Alachiotis

Bioinform., 2024

SoftCache: A Software Cache for PCIe-Attached Hardware Accelerators.

[BibT_eX]

[DOI]

Steven Wijnja

Proceedings of the Platform for Advanced Scientific Computing Conference, 2024

Accelerated Spiking Convolutional Neural Networks for Scalable Population Genomics.

[BibT_eX]

[DOI]

Proceedings of the 14th International Symposium on Highly Efficient Accelerators and Reconfigurable Technologies, 2024

Exploring the Versal AI Engines for Signal Processing in Radio Astronomy.

[BibT_eX]

[DOI]

Proceedings of the 34th International Conference on Field-Programmable Logic and Applications, 2024

Lightweight Instrumentation for Accurate Performance Monitoring in RTOSes.

[BibT_eX]

[DOI]

Proceedings of the Design, Automation & Test in Europe Conference & Exhibition, 2024

2023

A Survey of Processing Systems for Phylogenetics and Population Genetics.

[BibT_eX]

[DOI]

Reinout Corts

ACM Trans. Reconfigurable Technol. Syst., September, 2023

Genome-wide scans for selective sweeps using convolutional neural networks.

[BibT_eX]

[DOI]

Matthijs Leon Souilljee

Bioinform., 2023

SweepNet: A Lightweight CNN Architecture for the Classification of Adaptive Genomic Regions.

[BibT_eX]

[DOI]

Proceedings of the Platform for Advanced Scientific Computing Conference, 2023

Accelerated Real-Time Classification of Evolving Data Streams using Adaptive Random Forests.

[BibT_eX]

[DOI]

Frank Ridder

Kuan-Hsun Chen

Proceedings of the International Conference on Field Programmable Technology, 2023

FPGA-accelerated Quantum Transport Measurements.

[BibT_eX]

[DOI]

Timo Haarman

Antonio Sousa de Almeida

Amber Heskes

Floris Zwanenburg

Proceedings of the International Conference on Field Programmable Technology, 2023

An unprotected RISC-V Soft-core processor on an SRAM FPGA: Is it as bad as it sounds?

[BibT_eX]

[DOI]

Proceedings of the IEEE European Test Symposium, 2023

Exploring Genomic Sequence Alignment for Improving Side-Channel Analysis.

[BibT_eX]

[DOI]

Proceedings of the Computer Security - ESORICS 2023, 2023

Neutron Radiation Tests of the NEORV32 RISC-V SoC on Flash-Based FPGAs.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Symposium on Defect and Fault Tolerance in VLSI and Nanotechnology Systems, 2023

Effective Data Preprocessing Techniques for CNN-based Selective Sweep Detection.

[BibT_eX]

[DOI]

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2023

2022

Scalable Phylogeny Reconstruction with Disaggregated Near-memory Processing.

[BibT_eX]

[DOI]

Manolis Pissadakis

ACM Trans. Reconfigurable Technol. Syst., 2022

A novel approximation scheme for floating-point square root and inverse square root for FPGAs.

[BibT_eX]

[DOI]

Pietro Pennestrì

Yanqiu Huang

Proceedings of the 11th International Conference on Modern Circuits and Systems Technologies, 2022

Accelerated LD-based selective sweep detection using GPUs and FPGAs.

[BibT_eX]

[DOI]

Reinout Corts

Niek Sterenborg

Proceedings of the IEEE International Parallel and Distributed Processing Symposium, 2022

An Event-driven Recurrent Spiking Neural Network Architecture for Efficient Inference on FPGA.

[BibT_eX]

[DOI]

Proceedings of the ICONS 2022: International Conference on Neuromorphic Systems, Knoxville, TN, USA, July 27, 2022

2021

Accelerating Phylogenetics Using FPGAs in the Cloud.

[BibT_eX]

[DOI]

IEEE Micro, 2021

An Energy-Efficient FPGA-based Convolutional Neural Network Implementation.

[BibT_eX]

[DOI]

Hasan Irmak

Daniel Ziener

Proceedings of the 29th Signal Processing and Communications Applications Conference, 2021

EDRA: A Hardware-Assisted Decoupled Access/Execute Framework on the Digital Market - Invited Paper.

[BibT_eX]

[DOI]

Andreas Brokalakis

Proceedings of the Embedded Computer Systems: Architectures, Modeling, and Simulation, 2021

Increasing Flexibility of FPGA-based CNN Accelerators with Dynamic Partial Reconfiguration.

[BibT_eX]

[DOI]

Hasan Irmak

Daniel Ziener

Proceedings of the 31st International Conference on Field-Programmable Logic and Applications, 2021

Integrative hierarchical ensemble clustering for improved disease subtype discovery.

[BibT_eX]

[DOI]

Bastian Pfeifer

Andrei Voicu-Spineanu

Michael G. Schimek

Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine, 2021

2020

RAiSD-X: A Fast and Accurate FPGA System for the Detection of Positive Selection in Thousands of Genomes.

[BibT_eX]

[DOI]

Charalampos Vatsolakis

Grigorios Chrysos

ACM Trans. Reconfigurable Technol. Syst., 2020

Near-memory Acceleration for Scalable Phylogenetic Inference.

[BibT_eX]

[DOI]

Emmanouil Pissadakis

Sundeep Rangan

Proceedings of the FPGA '20: The 2020 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, 2020

qLD: High-performance Computation of Linkage Disequilibrium on CPU and GPU.

[BibT_eX]

[DOI]

Charalampos Theodoris

Tze Meng Low

Proceedings of the 20th IEEE International Conference on Bioinformatics and Bioengineering, 2020

Exploring Modern FPGA Platforms for Faster Phylogeny Reconstruction with RAxML.

[BibT_eX]

[DOI]

Proceedings of the 20th IEEE International Conference on Bioinformatics and Bioengineering, 2020

2019

Accelerating Binarized Convolutional Neural Networks with Dynamic Partial Reconfiguration on Disaggregated FPGAs.

[BibT_eX]

[DOI]

Emmanouil Pissadakis

Proceedings of the Parallel Computing: Technology Trends, 2019

2018

ReFiRe: Efficient Deployment of Remote Fine-Grained Reconfigurable Accelerators.

[BibT_eX]

[DOI]

Emmanouil Pissadakis

Thanasis Korakis

Proceedings of the International Conference on Field-Programmable Technology, 2018

Accelerated Inference of Positive Selection on Whole Genomes.

[BibT_eX]

[DOI]

Charalampos Vatsolakis

Grigorios Chrysos

Proceedings of the 28th International Conference on Field Programmable Logic and Applications, 2018

dReDBox: Materializing a full-stack rack-scale system prototype of a next-generation disaggregated datacenter.

[BibT_eX]

[DOI]

Dionisis N. Pnevmatikatos

Óscar González de Dios

Proceedings of the 2018 Design, Automation & Test in Europe Conference & Exhibition, 2018

REMAP: Remote mEmory Manager for disAggregated Platforms.

[BibT_eX]

[DOI]

Proceedings of the 29th IEEE International Conference on Application-specific Systems, 2018

2017

FPGA-based evaluation platform for disaggregated computing.

[BibT_eX]

[DOI]

Proceedings of the 2017 International Conference on Embedded Computer Systems: Architectures, 2017

Deploying FPGAs to future-proof genome-wide analyses based on linkage disequilibrium.

[BibT_eX]

[DOI]

Proceedings of the 27th International Conference on Field Programmable Logic and Applications, 2017

Versatile deployment of FPGA accelerators in disaggregated data centers: A bioinformatics case study.

[BibT_eX]

[DOI]

Proceedings of the 27th International Conference on Field Programmable Logic and Applications, 2017

Multi-FPGA Evaluation Platform for Disaggregated Computing.

[BibT_eX]

[DOI]

Proceedings of the 25th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines, 2017

2016

Efficient Computation of Linkage Disequilibria as Dense Linear Algebra Operations.

[BibT_eX]

[DOI]

Doru-Thom Popovici

Tze Meng Low

Proceedings of the 2016 IEEE International Parallel and Distributed Processing Symposium Workshops, 2016

High Performance Linkage Disequilibrium: FPGAs Hold the Key.

[BibT_eX]

[DOI]

Gabriel Weisz

Proceedings of the 2016 ACM/SIGDA International Symposium on Field-Programmable Gate Arrays, 2016

2015

Enabling portable energy efficiency with memory accelerated library.

[BibT_eX]

[DOI]

Proceedings of the 48th International Symposium on Microarchitecture, 2015

Generating FPGA accelerators for chemical similarity assessment.

[BibT_eX]

[DOI]

Proceedings of the 25th International Conference on Field Programmable Logic and Applications, 2015

2013

libgapmis: extending short-read alignments.

[BibT_eX]

[DOI]

Fernando Izquierdo-Carrasco

BMC Bioinform., 2013

A Generic Vectorization Scheme and a GPU Kernel for the Phylogenetic Likelihood Library.

[BibT_eX]

[DOI]

Proceedings of the 2013 IEEE International Symposium on Parallel & Distributed Processing, 2013

2012

Algorithms and Computer Architectures for Evolutionary Bioinformatics.

[BibT_eX]

[DOI]

PhD thesis, 2012

Coupling SIMD and SIMT architectures to boost performance of a phylogeny-aware alignment kernel.

[BibT_eX]

[DOI]

BMC Bioinform., 2012

OmegaPlus: a scalable tool for rapid detection of selective sweeps in whole-genome datasets.

[BibT_eX]

[DOI]

Bioinform., 2012

A versatile UDP/IP based PC ↔ FPGA communication platform.

[BibT_eX]

[DOI]

Proceedings of the 2012 International Conference on Reconfigurable Computing and FPGAs, 2012

An Optimized Reconfigurable System for Computing the Phylogenetic Likelihood Function on DNA Data.

[BibT_eX]

[DOI]

Proceedings of the 26th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, 2012

Exploiting Multi-grain Parallelism for Efficient Selective Sweep Detection.

[BibT_eX]

[DOI]

Proceedings of the Algorithms and Architectures for Parallel Processing, 2012

Libgapmis: An ultrafast library for short-read single-gap alignment.

[BibT_eX]

[DOI]

Proceedings of the 2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops, 2012

2011

A Vector-Like Reconfigurable Floating-Point Unit for the Logarithm.

[BibT_eX]

[DOI]

Int. J. Reconfigurable Comput., 2011

FPGA Acceleration of the Phylogenetic Parsimony Kernel?

[BibT_eX]

[DOI]

Proceedings of the International Conference on Field Programmable Logic and Applications, 2011

Accelerating Phylogeny-Aware Short DNA Read Alignment with FPGAs.

[BibT_eX]

[DOI]

Proceedings of the IEEE 19th Annual International Symposium on Field-Programmable Custom Computing Machines, 2011

FPGA Optimizations for a Pipelined Floating-Point Exponential Unit.

[BibT_eX]

[DOI]

Proceedings of the Reconfigurable Computing: Architectures, Tools and Applications, 2011

2010

Time and memory efficient likelihood-based tree searches on phylogenomic alignments with missing data.

[BibT_eX]

[DOI]

Bioinform., 2010

Efficient floating-point logarithm unit for FPGAs.

[BibT_eX]

[DOI]

Proceedings of the 24th IEEE International Symposium on Parallel and Distributed Processing, 2010

Efficient PC-FPGA Communication over Gigabit Ethernet.

[BibT_eX]

[DOI]

Proceedings of the 10th IEEE International Conference on Computer and Information Technology, 2010

2009

Exploring FPGAs for accelerating the phylogenetic likelihood function.

[BibT_eX]

[DOI]

Euripides Sotiriades

Apostolos Dollas

Proceedings of the 23rd IEEE International Symposium on Parallel and Distributed Processing, 2009

A reconfigurable architecture for the Phylogenetic Likelihood Function.

[BibT_eX]

[DOI]